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Genome evolution and evolutionary systems biology

Section edited by Maria Anisimova, Arndt von Haeseler and David Liberles

This section considers studies on genome evolution and systems biology approaches to determining evolutionary processes.

Page 4 of 10

  1. Clostridium difficile is a nosocomial pathogen prevalent in hospitals worldwide and increasingly common in the community. Sequence differences have been shown to be present in the Surf...

    Authors: Mark Lynch, Thomas A. Walsh, Izabela Marszalowska, Andrew E. Webb, Micheál MacAogain, Thomas R. Rogers, Henry Windle, Dermot Kelleher, Mary J. O’Connell and Christine E. Loscher

    Citation: BMC Evolutionary Biology 2017 17:90

    Content type: Research article

    Published on:

    The Erratum to this article has been published in BMC Evolutionary Biology 2017 17:135

  2. Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive o...

    Authors: Gloria I. Giraldo-Calderón, Michael J. Zanis and Catherine A. Hill

    Citation: BMC Evolutionary Biology 2017 17:84

    Content type: Research article

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  3. Mitochondrial introns intermit coding regions of genes and feature characteristic secondary structures and splicing mechanisms. In metazoans, mitochondrial introns have only been detected in sponges, cnidarian...

    Authors: Astrid Schuster, Jose V. Lopez, Leontine E. Becking, Michelle Kelly, Shirley A. Pomponi, Gert Wörheide, Dirk Erpenbeck and Paco Cárdenas

    Citation: BMC Evolutionary Biology 2017 17:82

    Content type: Research article

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  4. Changing environmental conditions pose a challenge for the survival of species. To meet this challenge organisms adapt their phenotype by physiological regulation (phenotypic plasticity) or by evolving. Regula...

    Authors: Thomas D. Cuypers, Jacob P. Rutten and Paulien Hogeweg

    Citation: BMC Evolutionary Biology 2017 17:60

    Content type: Research Article

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  5. In the history of population genetics balancing selection has been considered as an important evolutionary force, yet until today little is known about its abundance and its effect on patterns of genetic diver...

    Authors: Myriam Croze, Andreas Wollstein, Vedran Božičević, Daniel Živković, Wolfgang Stephan and Stephan Hutter

    Citation: BMC Evolutionary Biology 2017 17:15

    Content type: Research article

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  6. Chitin, the second most abundant biopolymer on earth after cellulose, is found in probably all fungi, many animals (mainly invertebrates), several protists and a few algae, playing an essential role in the dev...

    Authors: Isabelle R. Gonçalves, Sophie Brouillet, Marie-Christine Soulié, Simonetta Gribaldo, Catherine Sirven, Noémie Charron, Martine Boccara and Mathias Choquer

    Citation: BMC Evolutionary Biology 2016 16:252

    Content type: Research article

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  7. Opsins are the only class of proteins used for light perception in image-forming eyes. Gene duplication and subsequent functional divergence of opsins have played an important role in expanding photoreceptive ...

    Authors: Anita J. Porath-Krause, Autum N. Pairett, Davide Faggionato, Bhagyashree S. Birla, Kannan Sankar and Jeanne M. Serb

    Citation: BMC Evolutionary Biology 2016 16:250

    Content type: Research article

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  8. Bacterial endosymbionts are found across the eukaryotic kingdom and profoundly impacted eukaryote evolution. In many endosymbiotic associations with vertically inherited symbionts, highly complementary metabol...

    Authors: Jorge Morales, Sofia Kokkori, Diana Weidauer, Jarrod Chapman, Eugene Goltsman, Daniel Rokhsar, Arthur R. Grossman and Eva C. M. Nowack

    Citation: BMC Evolutionary Biology 2016 16:247

    Content type: Research article

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  9. From a mtDNA dominant perspective, the exit from Africa of modern humans to colonize Eurasia occurred once, around 60 kya, following a southern coastal route across Arabia and India to reach Australia short af...

    Authors: Patricia Marrero, Khaled K. Abu-Amero, Jose M. Larruga and Vicente M. Cabrera

    Citation: BMC Evolutionary Biology 2016 16:246

    Content type: Research article

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  10. Although bats are natural reservoirs of many pathogens, few studies have been conducted on the genetic variation and detection of selection in major histocompatibility complex (MHC) genes. These genes are crit...

    Authors: Arielle Salmier, Benoit de Thoisy, Brigitte Crouau-Roy, Vincent Lacoste and Anne Lavergne

    Citation: BMC Evolutionary Biology 2016 16:229

    Content type: Research article

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  11. In mouse ES cells, the function of Sox2 is essential for the maintenance of pluripotency. Since the Sox-family of transcription factors are well conserved in the animal kingdom, addressing the evolutionary ori...

    Authors: Hitoshi Niwa, Akira Nakamura, Makoto Urata, Maki Shirae-Kurabayashi, Shigehiro Kuraku, Steven Russell and Satoshi Ohtsuka

    Citation: BMC Evolutionary Biology 2016 16:173

    Content type: Research article

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  12. The development of multicellular organisms is coordinated by various gene regulatory mechanisms that ensure correct spatio-temporal patterns of gene expression. Recently, the role of antisense transcription in...

    Authors: Christian Rödelsperger, Kevin Menden, Vahan Serobyan, Hanh Witte and Praveen Baskaran

    Citation: BMC Evolutionary Biology 2016 16:165

    Content type: Research Article

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  13. Transitions from marine to intertidal and terrestrial habitats resulted in a significant adaptive radiation within the Panpulmonata (Gastropoda: Heterobranchia). This clade comprises several groups that invade...

    Authors: Pedro E. Romero, Alexander M. Weigand and Markus Pfenninger

    Citation: BMC Evolutionary Biology 2016 16:164

    Content type: Research article

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  14. Predicting adaptive trajectories is a major goal of evolutionary biology and useful for practical applications. Systems biology has enabled the development of genome-scale metabolic models. However, analysing ...

    Authors: Tobias Großkopf, Jessika Consuegra, Joël Gaffé, John C. Willison, Richard E. Lenski, Orkun S. Soyer and Dominique Schneider

    Citation: BMC Evolutionary Biology 2016 16:163

    Content type: Research article

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  15. A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartil...

    Authors: Ramray Bhat, Mahul Chakraborty, Tilmann Glimm, Thomas A. Stewart and Stuart A. Newman

    Citation: BMC Evolutionary Biology 2016 16:162

    Content type: Research article

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  16. A deeply rooted phylogenetic lineage of Mycobacterium tuberculosis (M. tuberculosis) termed lineage 7 was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was perf...

    Authors: Solomon A. Yimer, Amine Namouchi, Ephrem Debebe Zegeye, Carol Holm-Hansen, Gunnstein Norheim, Markos Abebe, Abraham Aseffa and Tone Tønjum

    Citation: BMC Evolutionary Biology 2016 16:146

    Content type: Research article

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  17. RLSB, an S-1 domain RNA binding protein of Arabidopsis, selectively binds rbcL mRNA and co-localizes with Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) within chloroplasts of C3 and C4 plants. Previou...

    Authors: Pradeep Yerramsetty, Matt Stata, Rebecca Siford, Tammy L. Sage, Rowan F. Sage, Gane Ka-Shu Wong, Victor A. Albert and James O. Berry

    Citation: BMC Evolutionary Biology 2016 16:141

    Content type: Research article

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  18. The major histocompatibility complex (MHC) plays a crucial role in the adaptive immune system and has been extensively studied across vertebrate taxa. Although the function of MHC genes appears to be conserved...

    Authors: Shandiya Balasubramaniam, Rebecca D. Bray, Raoul A. Mulder, Paul Sunnucks, Alexandra Pavlova and Jane Melville

    Citation: BMC Evolutionary Biology 2016 16:112

    Content type: Research article

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  19. Kinetoplastea is a diverse protist lineage composed of several of the most successful parasites on Earth, organisms whose metabolisms have coevolved with those of the organisms they infect. Parasitic kinetopla...

    Authors: Ugo Cenci, Daniel Moog, Bruce A. Curtis, Goro Tanifuji, Laura Eme, Julius Lukeš and John M. Archibald

    Citation: BMC Evolutionary Biology 2016 16:109

    Content type: Research article

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  20. Arthropods have received much attention as a model for studying opsin evolution in invertebrates. Yet, relatively few studies have investigated the diversity of opsin proteins that underlie spectral sensitivit...

    Authors: Nathan P. Lord, Rebecca L. Plimpton, Camilla R. Sharkey, Anton Suvorov, Jonathan P. Lelito, Barry M. Willardson and Seth M. Bybee

    Citation: BMC Evolutionary Biology 2016 16:107

    Content type: Research article

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  21. The Planar Cell Polarity pathway (PCP) has been described as the main feature involved in patterning cell orientation in bilaterian tissues. Recently, a similar phenomenon was revealed in cnidarians, in which ...

    Authors: Quentin Schenkelaars, Laura Fierro-Constain, Emmanuelle Renard and Carole Borchiellini

    Citation: BMC Evolutionary Biology 2016 16:69

    Content type: Research article

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  22. Neuropeptides are key players in information transfer and act as important regulators of development, growth, metabolism, and reproduction within multi-cellular animal organisms (Metazoa). These short protein-...

    Authors: Christian Derst, Heinrich Dircksen, Karen Meusemann, Xin Zhou, Shanlin Liu and Reinhard Predel

    Citation: BMC Evolutionary Biology 2016 16:51

    Content type: Research article

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  23. Nuclear genes of euglenids contain two major types of introns: conventional spliceosomal and nonconventional introns. The latter are characterized by variable non-canonical borders, RNA secondary structure tha...

    Authors: Rafał Milanowski, Natalia Gumińska, Anna Karnkowska, Takao Ishikawa and Bożena Zakryś

    Citation: BMC Evolutionary Biology 2016 16:49

    Content type: Research article

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  24. Low complexity regions (LCRs) are a ubiquitous feature in genomes and yet their evolutionary history and functional roles are unclear. Previous studies have shown contrasting evidence in favor of both neutral ...

    Authors: Fabia U. Battistuzzi, Kristan A. Schneider, Matthew K. Spencer, David Fisher, Sophia Chaudhry and Ananias A. Escalante

    Citation: BMC Evolutionary Biology 2016 16:47

    Content type: Research article

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  25. Understanding the evolutionary forces that influence variation in gene regulatory regions in natural populations is an important challenge for evolutionary biology because natural selection for such variations...

    Authors: Mitsuhiko P. Sato, Takashi Makino and Masakado Kawata

    Citation: BMC Evolutionary Biology 2016 16:35

    Content type: Research article

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  26. The increasing abundance of sequence data has exacerbated a long known problem: gene trees and species trees for the same terminal taxa are often incongruent. Indeed, genes within a genome have not all followe...

    Authors: Beatriz Mengual-Chuliá, Stéphanie Bedhomme, Guillaume Lafforgue, Santiago F. Elena and Ignacio G. Bravo

    Citation: BMC Evolutionary Biology 2016 16:32

    Content type: Research article

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  27. Multicellularity evolved multiple times in eukaryotes. In all cases, this required an elaboration of the regulatory mechanisms controlling gene expression. Amongst the conserved eukaryotic transcription factor...

    Authors: Katia Jindrich and Bernard M. Degnan

    Citation: BMC Evolutionary Biology 2016 16:28

    Content type: Research article

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  28. Prions are transmissible, propagating alternative states of proteins, and are usually made from the fibrillar, beta-sheet-rich assemblies termed amyloid. Prions in the budding yeast Saccharomyces cerevisiae propa...

    Authors: Lu An, David Fitzpatrick and Paul M. Harrison

    Citation: BMC Evolutionary Biology 2016 16:24

    Content type: Research article

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  29. RNA editing by cytidine-to-uridine conversions is an essential step of RNA maturation in plant organelles. Some 30–50 sites of C-to-U RNA editing exist in chloroplasts of flowering plant models like Arabidopsis, ...

    Authors: Anke Hein, Monika Polsakiewicz and Volker Knoop

    Citation: BMC Evolutionary Biology 2016 16:23

    Content type: Research article

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  30. Protamines are sperm nuclear proteins with a crucial role in chromatin condensation. Their function is strongly linked to sperm head morphology and male fertility. Protamines appear to be affected by a complex...

    Authors: Lena Lüke, Maximiliano Tourmente, Hernan Dopazo, François Serra and Eduardo R. S. Roldan

    Citation: BMC Evolutionary Biology 2016 16:21

    Content type: Research article

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  31. Many prokaryotic kinases that phosphorylate small molecule substrates, such as antibiotics, lipids and sugars, are evolutionarily related to Eukaryotic Protein Kinases (EPKs). These Eukaryotic-Like Kinases (EL...

    Authors: Krishnadev Oruganty, Eric E. Talevich, Andrew F. Neuwald and Natarajan Kannan

    Citation: BMC Evolutionary Biology 2016 16:7

    Content type: Research article

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  32. Transporter proteins are predicted to have an important role in the mycorrhizal symbiosis, due to the fact that this type of an interaction between plants and fungi requires a continuous nutrient and signallin...

    Authors: Andriy Kovalchuk, Annegret Kohler, Francis Martin and Fred O. Asiegbu

    Citation: BMC Evolutionary Biology 2015 15:249

    Content type: Research article

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  33. Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. ...

    Authors: Dorothée Huchon, Amir Szitenberg, Sigal Shefer, Micha Ilan and Tamar Feldstein

    Citation: BMC Evolutionary Biology 2015 15:278

    Content type: Research article

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  34. A deeper understanding of differences and similarities in transcriptional regulation between species can uncover important information about gene functions and the role of genes in disease. Deciphering such pa...

    Authors: Gianni Monaco, Sipko van Dam, João Luis Casal Novo Ribeiro, Anis Larbi and João Pedro de Magalhães

    Citation: BMC Evolutionary Biology 2015 15:259

    Content type: Research article

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  35. Bacillus cereus sensu lato comprises eight closely related species including the human pathogens Bacillus anthracis and Bacillus cereus. Within B. cereus sensu lato, chromosomally and ...

    Authors: Maria-Elisabeth Böhm, Christopher Huptas, Viktoria Magdalena Krey and Siegfried Scherer

    Citation: BMC Evolutionary Biology 2015 15:246

    Content type: Research article

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  36. Sex chromosomes of extant eutherian species are too ancient to reveal the process that initiated sex-chromosome differentiation. By contrast, the neo-sex chromosomes generated by sex-autosome fusions of recent...

    Authors: Chie Murata, Yoko Kuroki, Issei Imoto, Masaru Tsukahara, Naoto Ikejiri and Asato Kuroiwa

    Citation: BMC Evolutionary Biology 2015 15:234

    Content type: Research article

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  37. Selection on proteins is typically measured with the assumption that each protein acts independently. However, selection more likely acts at higher levels of biological organization, requiring an integrative v...

    Authors: Russell A. Hermansen, Brian K. Mannakee, Wolfgang Knecht, David A. Liberles and Ryan N. Gutenkunst

    Citation: BMC Evolutionary Biology 2015 15:232

    Content type: Research article

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  38. USP4, USP15 and USP11 are paralogous deubiquitinating enzymes as evidenced by structural organization and sequence similarity. Based on known interactions and substrates it would appear that they have partiall...

    Authors: Caitlyn Vlasschaert, Xuhua Xia, Josée Coulombe and Douglas A. Gray

    Citation: BMC Evolutionary Biology 2015 15:230

    Content type: Research article

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  39. Defining factors that contributed to the fixation of a high number of underdominant chromosomal rearrangements is a complex task because not only molecular mechanisms must be considered, but also the uniquenes...

    Authors: Cibele G. Sotero-Caio, Marianne Volleth, Federico G. Hoffmann, LuAnn Scott, Holly A. Wichman, Fengtang Yang and Robert J. Baker

    Citation: BMC Evolutionary Biology 2015 15:220

    Content type: Research article

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  40. Poly(A)-binding proteins (PABPs) are evolutionarily conserved proteins that have important functions in the regulation of translation and the control of mRNA stability in eukaryotes. Most PABPs encode a C-term...

    Authors: Domingo Jiménez-López, Jaime Bravo and Plinio Guzmán

    Citation: BMC Evolutionary Biology 2015 15:195

    Content type: Research article

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  41. The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of vir...

    Authors: Izza Nasrullah, Azeem M Butt, Shifa Tahir, Muhammad Idrees and Yigang Tong

    Citation: BMC Evolutionary Biology 2015 15:174

    Content type: Research article

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  42. Analyzed individually, gene trees for a given taxon set tend to harbour incongruent or conflicting signals. One popular approach to deal with this circumstance is to use concatenated data. But especially in pr...

    Authors: Thorsten Thiergart, Giddy Landan and William F Martin

    Citation: BMC Evolutionary Biology 2014 14:266

    Content type: Research article

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  43. X chromosome inactivation is the transcriptional silencing of one X chromosome in the somatic cells of female mammals. In eutherian mammals (e.g. humans) one of the two X chromosomes is randomly chosen for sil...

    Authors: Claudia L Rodríguez-Delgado, Shafagh A Waters and Paul D Waters

    Citation: BMC Evolutionary Biology 2014 14:267

    Content type: Research article

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